BioNanotechnology Seminar Series - Fall 2012

Functional DNA Nanotechnology: Precise Spatial and Dynamic Control of Nanomaterials Assembly and its Applications in Sensing, Imaging and Targeted Drug Delivery

Dr. Yi Lu
Department of Chemistry, Biochemistry, Bioengineering, Materials Science and Engineering, and Beckman Institute for Advanced Science and Technology

Tuesday, December 11, 2012
1000 MNTL, 12:00 - 1:00 PM

Abstract: Cell Genetic control of the assembly and disassembly of complex biological structures in response to internal chemical or biological stimuli under ambient conditions have been one of the hallmarks of biology. While proteins play a central role in natural biomaterials, synthetic nanomaterials assembled by nucleic acids are emerging in recent years. DNA has been shown to be highly programmable molecules resulting in a number of 2D and 3D nanostructures. Despite the promise, functionalizing these structures has been challenging. We have developed a novel method of using phosphorothioate DNA as anchors, and a bifunctional linker as a rigid molecular fastener that can connect gold nanoparticles to specific locations on the DNA backbone. Precise distance controls between two nanoparticles or proteins with nanometer resolution have been demonstrated. We are also elucidating DNA "genetic codes" for nanomaterials.

In addition to precise spatial control, dynamic control of the assembly of nanomaterials in response to internal stimuli under ambient conditions is quite important for 3D assembly. To meet this challenge, we took advantage of recent advance in biology, i.e., discovery of functional DNA, a new class of DNAs that can either bind to a target molecule (known as aptamers) or perform catalytic reactions (known as DNAzymes), that are very specific for a wide range of targets, and demonstrated the use of these functional DNA for dynamic control of assembly of gold nanoparticles, iron oxide nanoparticles, quantum dots, and nanotubes, in response to a wide range of chemical and biological stimuli from small metal ions to large biomolecules, including cancer cell markers. Because these nanomaterials possess unique optical, electrical, magnetic and catalytic properties, these systems have been converted into colorimetric, fluorescent, electrochemical sensors, and magnetic resonance imaging agents for detection of a broad range of analytes with high sensitivity and selectivity. The application of functional DNA nanotechnology has also been expanded to include targeted drug delivery.


A Materials Approach to Deconstructing the Stem Cell Microenvironment

Dr. Kristopher A. Kilian
Department of Materials Science and Engineering

Tuesday, November 27, 2012
1000 MNTL, 12:00 - 1:00 PM

Abstract: Cell culture materials that are engineered at the molecular, nano and micro scale can be used to guide pathways associated with cell fate specification. In this presentation, I will discuss our efforts in designing surfaces for studying signaling in adherent mesenchymal stem cells (MSCs). First I will show how soft lithography can be used to capture single stem cells in precise geometries to study how cell shape influences fate. MSCs cultured in small islands become quiescent and express elevated levels of multipotency markers; MSCs that are allowed to spread and proliferate express higher levels of osteogenesis markers. Using small molecule inhibitors of actomyosin contractility, we find that reduced cytoskeletal tension promotes maintenance of multipotency. Next I will demonstrate how cell geometry, matrix mechanics and ligand composition can be used together to maximize preferred differentiation outcomes. Cells that are cultured on polyacrylamide hydrogels express markers for both osteogenesis and myogenesis. By modulating the geometry of single MSCs on these hydrogel substrates we can preferentially direct specific differentiation outcomes. Finally, I will present our work using nanostructured porous silicon substrates to engineer the adhesion microenvironment for directing the fate of MSCs. Using these engineering approaches we can recapitulate aspects of the stem cell microenvironment to decipher the mechanochemical signals that direct cell fate.


Understanding and Controlling Fibrotic Myocardium

Dr. Guy M. Genin
Department of Mechanical Engineering & Materials Science, Washington University in St. Louis
Department of Neurological Surgery, Washington University School of Medicine

Tuesday, October 30, 2012
1000 MNTL, 12:00 - 1:00 PM

Abstract: Hypertension kills 1 in every 5000 Americans each year and affects the majority of those over the age of 55. Following prolonged hypertension, cardiac fibroblasts within the heart convert to myofibroblasts, a larger, contractile phenotype that produces fibrous connective tissue and thereby stiffens heart muscle. In addition to this mechanical effect, myofibroblasts disrupt normal patterns of electrical excitation of cardiomyoctyes, potentially leading to cardiac failure through any of several pathways. Therapies that control myofibroblasts would evidently be of value, but little is known about their mechanical and electrophysiological interactions with cardiomyocytes. We therefore developed and analyzed a model tissue system that allows us to dissect how myofibroblasts, cardiomyocytes, and ECM interface to alter the functioning of myocardium. This talk will summarize results suggesting pathways by which myofibroblasts alter the contractile response of myocardium, and some initial thoughts on treatments to improve this response by regulating cytoskeletal elements of myofibroblasts.


Improving the Sensitivity of Nanopatterned SERS Sensors by Promoting Surface Wetting

William Goldshlag, Electrical and Computer Engineering

Tuesday, October 23, 2012
1000 MNTL, 12:00 - 12:30 PM

Abstract: Nanopatterned metal surfaces are widely used for chemical sensing. One representative technique is surface-enhanced Raman spectroscopy (SERS). When analyte is placed on a solid substrate covered with densely packed metal nanoparticles, the intensity of Raman-scattered light increases by multiple orders of magnitude. However, such enhancement is highly spatially non-uniform and is concentrated in the nanogaps between adjacent particles. The ability of analyte molecules to diffuse into the regions of highest enhancement, therefore, limits the effectiveness of textured surfaces as chemical sensors. In liquid phase sensing, this is often determined by the ability of the solvent to completely wet the nanostructures.

In this talk, I will present my recent work in the analysis and promotion of surface wetting of dense arrays of gold nanodomes. I will discuss multiple approaches to nanodome wetting that focus either on the substrate or on the solvent. Finally, I will report, for the first time, label-free SERS detection of 25-base-long DNA strands on nanodomes substrates that became possible with the improved wetting. This marks an important milestone on the path of developing SERS nanodomes into a universal label-free DNA aptamer-based sensing platform.


Towards the Development of Click Chemistry-Mediated Nanomedicine for Cancer Cell Targeting

Vahid Mirshafiee, Chemical and Biomolecular Engineering

Tuesday, October 23, 2012
1000 MNTL, 12:30 - 1:00 PM

Abstract: Nanoparticulate delivery vehicles for cancer targeting and therapy are routinely prepared by incorporating a targeting ligand, such as an antibody or aptamer, to the surface of nanoparticles. The interaction between the targeting ligand and specific receptor on the cell membrane is anticipated to drive the nanoparticles to preferentially accumulate in tumor tissues, which enhances antitumor efficacy. However, this design has one major drawback; nanoparticles containing targeting ligands usually have substantially enhanced, undesirable retention in the spleen and liver as compared to unmodified nanoparticles. This undesirable biodistribution of the modified nanoparticles prohibits their in vivo targeting, resulting in increased immune response and reduced anticancer efficacy. To address this problem, we are investigating the use of click chemistry for targeted drug delivery.

We have developed nanoparticles that are functionalized with highly-strained and highly-reactive cycloalkynes. These functionalized nanoparticles undergo spontaneous, reagent-free covalent reaction with metabolically incorporated azido-sugars on the cell surface, which is anticipated to promote nanoparticles internalization through endocytosis. This approach is expected to allow high cellular uptake of the nanoparticles while triggering a lower immune response than nanoparticles functionalized with protein- or aptamer-based targeting ligands. Here we report our progress towards achieving these goals.


The Value of an International Research Experience and How it Can Change Your Approach to Research

Heather Huntsman, Kinesiology and Community Health
Samantha Knoll, Mechanical Science and Engineering

Tuesday, October 9, 2012
1000 MNTL, 12:00 - 1:00 PM

Abstract: Heather and Samantha spent part of Summer 2012 at the Max Planck Institute in Germany. In this presentation they discuss the value of international collaborative experiences for all graduate students.


DNAzymes as Novel Tools for Metal-Ion Sensing in Living Cells

Peiwen Wu, Biochemistry

Tuesday, September 25, 2012
1000 MNTL, 12:00 - 12:30 PM

Abstract: Solely considered as a generic storage material, DNA was discovered to be capable of carrying out catalytic or enzymatic functions in 1990s. Since then, DNAzymes specific for a wide range of bioavailable metal ions have been selected through in vitro selection and have been converted into a large number of metal-ion specific sensors for environmental detection. Such a development has significantly expanded the number of metal ions one can detect. However, despite of such advancement, no report on using DNAzymes for cellular detection and actuation has been reported. In this talk, we will discuss the strategies and demonstrations for metal-ion sensing in living cells using DNAzymes. Nanoparticle-based DNAzyme probes, as well as photoactivatable DNAzymes have shown to be promising tools for intracellular metal-ion sensing.


Label-Free Electronic Detection of microRNA Using Silicon Nanowire Arrays

Brian Dorvel, Biophysics

Tuesday, September 25, 2012
1000 MNTL, 12:30 - 1:00 PM

Abstract: Improving the performance and lowering the analyte detection limits of optical and electronic biosensors is essential for advancing wide ranging applications in diagnostics and drug discovery. One of these diagnostic platforms, based upon microfluidics coupled to ion-selective field effect transistors (ISFET's) offer great potential to address some world health goals since they can be made portable, low-cost, miniaturized, and sensitive. One of the biological targets of interest is miRNA, a small RNA which helps regulate protein expression, and its over or underexpression is commonly represented in multiple forms of cancer. Unfortunately, a number of performance issues, such as gate leakage and current instability due to fluid contact, have prevented widespread adoption of the technology for routine use. By using high-k dielectrics, such as hafnium oxide (HfO2), we have been able to address these challenges by passivating the exposed surfaces against destabilizing concerns of ion transport. With these fundamental stability issues addressed, we have created a fabrication process for HfO2 dielectric-based silicon nanowires for the detection of miRNA down to femtomolar levels.


Mechanical Property Characterization for 3D Collagen Cancer Cell Cultures

Yue Wang, Bioengineering

Tuesday, September 11, 2012
1000 MNTL, 12:00 - 12:30 PM

Abstract: The tumor microenvironment is mechanically modified during cancer progression. Imaging of tumor mechanical environment will provide new information for early cancer diagnosis. However, it is less clear how the mechanical environment is tuned in cancer. The goal of this study is to understand more clearly the contrast mechanisms of elasticity images in terms of molecular and cellular activities that drive cancer. Two imaging modalities (ultrasound and OCT) were implemented. These techniques have shown promise for discrimination between benign and malignant breast lesions, liver fibrosis staging and so on. This talk will focus on developing the imaging technique to image the mechanical properties in 3D collagen hydrogel with cancer cell cultures. The success of this new technique will provide quantitative mechanical property information of ECM in the cellular level, and hopefully could monitor the mechanical influence during cancer progression and metastasis.